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No commits in common. "main" and "v1.3.2" have entirely different histories.
15
.cspell.json
15
.cspell.json
@ -1,14 +1,7 @@
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{
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{
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"version": "0.2",
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"version": "0.2",
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"language": "en,en-gb",
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"language": "en,en-gb",
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"ignoreWords": [
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"ignoreWords": ["followlinks", "getframe", "pycache", "pydantic", "UNLCK"],
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"followlinks",
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"getframe",
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"pycache",
|
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"pydantic",
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"toolbelt",
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"UNLCK"
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],
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"words": [
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"words": [
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"chacl",
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"chacl",
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"kikan",
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"kikan",
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@ -16,11 +9,7 @@
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"mdrsclient",
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"mdrsclient",
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"neurodata",
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"neurodata",
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"Neuroinformatics",
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"Neuroinformatics",
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"orcid",
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"RIKEN"
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"RIKEN"
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],
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],
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"ignorePaths": [
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"ignorePaths": [".env", "__pycache__"]
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".env",
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"__pycache__"
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]
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}
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}
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3
.gitignore
vendored
3
.gitignore
vendored
@ -160,5 +160,4 @@ cython_debug/
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.idea/
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.idea/
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# mdrs-cli
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# mdrs-cli
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.neurodatacli.config
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.neurodatacli.config
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poetry.toml
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|
@ -1,6 +1,6 @@
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MIT License
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MIT License
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|
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Copyright (c) 2023- Neuroinformatics Unit, RIKEN CBS
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Copyright (c) 2023 Neuroinformatics Unit, RIKEN CBS
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Permission is hereby granted, free of charge, to any person obtaining a copy
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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of this software and associated documentation files (the "Software"), to deal
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17
README.md
17
README.md
@ -60,7 +60,7 @@ List the folder contents
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```shell
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```shell
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mdrs ls neurodata:/NIU/Repository/
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mdrs ls neurodata:/NIU/Repository/
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mdrs ls -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/
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mdrs ls -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/
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mdrs ls -r neurodata:/NIU/Repository/Dataset1/
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mdrs ls -r neurodata:/NIU/Repository/Dataset1/
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mdrs ls -J -r neurodata:/NIU/Repository/Dataset1/
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mdrs ls -J -r neurodata:/NIU/Repository/Dataset1/
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```
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```
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@ -80,7 +80,6 @@ Upload the file or directory
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```shell
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```shell
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mdrs upload ./sample.dat neurodata:/NIU/Repository/TEST/
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mdrs upload ./sample.dat neurodata:/NIU/Repository/TEST/
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mdrs upload -r ./dataset neurodata:/NIU/Repository/TEST/
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mdrs upload -r ./dataset neurodata:/NIU/Repository/TEST/
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mdrs upload -r --skip-if-exists ./dataset neurodata:/NIU/Repository/TEST/
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```
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```
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### download
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### download
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@ -90,9 +89,7 @@ Download the file or folder
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```shell
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```shell
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mdrs download neurodata:/NIU/Repository/TEST/sample.dat ./
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mdrs download neurodata:/NIU/Repository/TEST/sample.dat ./
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mdrs download -r neurodata:/NIU/Repository/TEST/dataset/ ./
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mdrs download -r neurodata:/NIU/Repository/TEST/dataset/ ./
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mdrs download -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.dat ./
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mdrs download -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.dat ./
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mdrs download -r --exclude /NIU/Repository/TEST/dataset/skip neurodata:/NIU/Repository/TEST/dataset/ ./
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mdrs download -r --skip-if-exists neurodata:/NIU/Repository/TEST/dataset/ ./
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```
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```
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### mv
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### mv
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@ -118,8 +115,8 @@ mdrs cp -r neurodata:/NIU/Repository/TEST/dataset neurodata:/NIU/Repository/TEST
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Remove the file or folder
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Remove the file or folder
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```shell
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```shell
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mdrs rm neurodata:/NIU/Repository/TEST/sample.dat
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mdrs rm neurodata:/NIU/Repository/TEST2/sample2.dat
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mdrs rm -r neurodata:/NIU/Repository/TEST/dataset
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mdrs rm -r neurodata:/NIU/Repository/TEST2/dataset
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```
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```
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### chacl
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### chacl
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@ -129,7 +126,7 @@ Change the folder access level
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```shell
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```shell
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mdrs chacl private neurodata:/NIU/Repository/Private
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mdrs chacl private neurodata:/NIU/Repository/Private
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mdrs chacl cbs_open -r neurodata:/NIU/Repository/CBS_Open
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mdrs chacl cbs_open -r neurodata:/NIU/Repository/CBS_Open
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mdrs chacl pw_open -r -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open
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mdrs chacl pw_open -r -p FOLDER_PASSWORD neurodata:/NIU/Repository/PW_Open
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```
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```
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### metadata
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### metadata
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@ -138,7 +135,7 @@ Get a folder metadata
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```shell
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```shell
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mdrs metadata neurodata:/NIU/Repository/TEST/
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mdrs metadata neurodata:/NIU/Repository/TEST/
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mdrs metadata -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/
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mdrs metadata -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/
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```
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```
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### file-metadata
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### file-metadata
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@ -147,7 +144,7 @@ Get the file metadata
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```shell
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```shell
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mdrs file-metadata neurodata:/NIU/Repository/TEST/dataset/sample.dat
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mdrs file-metadata neurodata:/NIU/Repository/TEST/dataset/sample.dat
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mdrs file-metadata -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.txt
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mdrs file-metadata -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.txt
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```
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```
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### help
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### help
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|
@ -1 +1 @@
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1.3.11
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1.3.1
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@ -1,6 +1,5 @@
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import argparse
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import argparse
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import sys
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import sys
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from json import JSONDecodeError
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from mdrsclient.commands import (
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from mdrsclient.commands import (
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ChaclCommand,
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ChaclCommand,
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@ -53,9 +52,6 @@ def main() -> None:
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except MDRSException as e:
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except MDRSException as e:
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print(f"Error: {e}")
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print(f"Error: {e}")
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sys.exit(2)
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sys.exit(2)
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except JSONDecodeError:
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print("Unexpected response returned. Please check the configuration or the server's operational status.")
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sys.exit(2)
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except KeyboardInterrupt:
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except KeyboardInterrupt:
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sys.exit(130)
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sys.exit(130)
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@ -1,10 +1,8 @@
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import mimetypes
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import os
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import os
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from typing import Any, Final
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from typing import Any, Final
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from pydantic import TypeAdapter
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from pydantic import TypeAdapter
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from pydantic.dataclasses import dataclass
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from pydantic.dataclasses import dataclass
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from requests_toolbelt.multipart.encoder import MultipartEncoder
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from mdrsclient.api.base import BaseApi
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from mdrsclient.api.base import BaseApi
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from mdrsclient.api.utils import token_check
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from mdrsclient.api.utils import token_check
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@ -19,7 +17,6 @@ class FilesApiCreateResponse:
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class FilesApi(BaseApi):
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class FilesApi(BaseApi):
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ENTRYPOINT: Final[str] = "v3/files/"
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ENTRYPOINT: Final[str] = "v3/files/"
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FALLBACK_MIMETYPE: Final[str] = "application/octet-stream"
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def retrieve(self, id: str) -> File:
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def retrieve(self, id: str) -> File:
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# print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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# print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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@ -33,43 +30,30 @@ class FilesApi(BaseApi):
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# print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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# print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT
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url = self.ENTRYPOINT
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token_check(self.connection)
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token_check(self.connection)
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data: dict[str, str | int] | MultipartEncoder = {}
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data: dict[str, str | int] = {"folder_id": folder_id}
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try:
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try:
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with open(os.path.realpath(path), mode="rb") as fp:
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with open(os.path.realpath(path), mode="rb") as fp:
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data = MultipartEncoder(
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response = self.connection.post(url, data=data, files={"file": fp})
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fields={"folder_id": folder_id, "file": (os.path.basename(path), fp, self._get_mime_type(path))}
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)
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response = self.connection.post(url, data=data, headers={"Content-Type": data.content_type})
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self._raise_response_error(response)
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self._raise_response_error(response)
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ret = TypeAdapter(FilesApiCreateResponse).validate_python(response.json())
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ret = TypeAdapter(FilesApiCreateResponse).validate_python(response.json())
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except OSError:
|
except OSError:
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raise UnexpectedException(f"Could not open `{path}` file.")
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raise UnexpectedException(f"Could not open `{path}` file.")
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except MemoryError:
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raise UnexpectedException("Out of memory.")
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except Exception as e:
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raise UnexpectedException("Unspecified error.") from e
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return ret.id
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return ret.id
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def update(self, file: File, path: str | None) -> bool:
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def update(self, file: File, path: str | None) -> bool:
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# print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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# print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + file.id + "/"
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url = self.ENTRYPOINT + file.id + "/"
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token_check(self.connection)
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token_check(self.connection)
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data: dict[str, str | int] | MultipartEncoder = {}
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if path is not None:
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if path is not None:
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# update file body
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# update file body
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try:
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try:
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with open(os.path.realpath(path), mode="rb") as fp:
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with open(os.path.realpath(path), mode="rb") as fp:
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data = MultipartEncoder(fields={"file": (os.path.basename(path), fp, self._get_mime_type(path))})
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response = self.connection.put(url, files={"file": fp})
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response = self.connection.put(url, data=data, headers={"Content-Type": data.content_type})
|
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except OSError:
|
except OSError:
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raise UnexpectedException(f"Could not open `{path}` file.")
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raise UnexpectedException(f"Could not open `{path}` file.")
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except MemoryError:
|
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raise UnexpectedException("Out of memory.")
|
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except Exception as e:
|
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raise UnexpectedException("Unspecified error.") from e
|
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else:
|
else:
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# update metadata
|
# update metadata
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data = {"name": file.name, "description": file.description}
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data: dict[str, str | int] = {"name": file.name, "description": file.description}
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response = self.connection.put(url, data=data)
|
response = self.connection.put(url, data=data)
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self._raise_response_error(response)
|
self._raise_response_error(response)
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return True
|
return True
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@ -111,7 +95,6 @@ class FilesApi(BaseApi):
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def download(self, file: File, path: str) -> bool:
|
def download(self, file: File, path: str) -> bool:
|
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# print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
|
# print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = file.download_url
|
url = file.download_url
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token_check(self.connection)
|
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response = self.connection.get(url, stream=True)
|
response = self.connection.get(url, stream=True)
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self._raise_response_error(response)
|
self._raise_response_error(response)
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try:
|
try:
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@ -123,9 +106,3 @@ class FilesApi(BaseApi):
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except PermissionError:
|
except PermissionError:
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print(f"Cannot create file `{path}`: Permission denied.")
|
print(f"Cannot create file `{path}`: Permission denied.")
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return True
|
return True
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|
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def _get_mime_type(self, path: str) -> str:
|
|
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mt = mimetypes.guess_type(path)
|
|
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if mt:
|
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return mt[0] or self.FALLBACK_MIMETYPE
|
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return self.FALLBACK_MIMETYPE
|
|
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|
@ -20,10 +20,8 @@ class UsersCurrentResponseLaboratory:
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class UsersApiCurrentResponse:
|
class UsersApiCurrentResponse:
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id: int
|
id: int
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username: str
|
username: str
|
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first_name: str
|
full_name: str
|
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last_name: str
|
|
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email: str
|
email: str
|
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orcid_id: str
|
|
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laboratories: list[UsersCurrentResponseLaboratory]
|
laboratories: list[UsersCurrentResponseLaboratory]
|
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is_staff: bool
|
is_staff: bool
|
||||||
is_active: bool
|
is_active: bool
|
||||||
|
@ -25,11 +25,11 @@ class ConfigCommand(BaseCommand):
|
|||||||
update_parser.add_argument("url", help="API entrypoint url of remote host")
|
update_parser.add_argument("url", help="API entrypoint url of remote host")
|
||||||
update_parser.set_defaults(func=cls.func_update)
|
update_parser.set_defaults(func=cls.func_update)
|
||||||
# config list
|
# config list
|
||||||
list_parser = config_parsers.add_parser("list", help="list all the remote hosts", aliases=["ls"])
|
list_parser = config_parsers.add_parser("list", help="list all the remote hosts")
|
||||||
list_parser.add_argument("-l", "--long", help="show the api url", action="store_true")
|
list_parser.add_argument("-l", "--long", help="show the api url", action="store_true")
|
||||||
list_parser.set_defaults(func=cls.func_list)
|
list_parser.set_defaults(func=cls.func_list)
|
||||||
# config delete
|
# config delete
|
||||||
delete_parser = config_parsers.add_parser("delete", help="delete an existing remote host", aliases=["remove"])
|
delete_parser = config_parsers.add_parser("delete", help="delete an existing remote host")
|
||||||
delete_parser.add_argument("remote", help="label of remote host")
|
delete_parser.add_argument("remote", help="label of remote host")
|
||||||
delete_parser.set_defaults(func=cls.func_delete)
|
delete_parser.set_defaults(func=cls.func_delete)
|
||||||
|
|
||||||
|
@ -8,8 +8,8 @@ from pydantic.dataclasses import dataclass
|
|||||||
from mdrsclient.api import FilesApi, FoldersApi
|
from mdrsclient.api import FilesApi, FoldersApi
|
||||||
from mdrsclient.commands.base import BaseCommand
|
from mdrsclient.commands.base import BaseCommand
|
||||||
from mdrsclient.connection import MDRSConnection
|
from mdrsclient.connection import MDRSConnection
|
||||||
from mdrsclient.exceptions import IllegalArgumentException, UnexpectedException
|
from mdrsclient.exceptions import IllegalArgumentException
|
||||||
from mdrsclient.models import File, Folder, Laboratory
|
from mdrsclient.models import File
|
||||||
from mdrsclient.settings import CONCURRENT
|
from mdrsclient.settings import CONCURRENT
|
||||||
|
|
||||||
|
|
||||||
@ -19,13 +19,6 @@ class DownloadFileInfo:
|
|||||||
path: str
|
path: str
|
||||||
|
|
||||||
|
|
||||||
@dataclass
|
|
||||||
class DownloadContext:
|
|
||||||
hasError: bool
|
|
||||||
isSkipIfExists: bool
|
|
||||||
files: list[DownloadFileInfo]
|
|
||||||
|
|
||||||
|
|
||||||
class DownloadCommand(BaseCommand):
|
class DownloadCommand(BaseCommand):
|
||||||
@classmethod
|
@classmethod
|
||||||
def register(cls, parsers: Any) -> None:
|
def register(cls, parsers: Any) -> None:
|
||||||
@ -33,15 +26,6 @@ class DownloadCommand(BaseCommand):
|
|||||||
download_parser.add_argument(
|
download_parser.add_argument(
|
||||||
"-r", "--recursive", help="download folders and their contents recursive", action="store_true"
|
"-r", "--recursive", help="download folders and their contents recursive", action="store_true"
|
||||||
)
|
)
|
||||||
download_parser.add_argument(
|
|
||||||
"-s",
|
|
||||||
"--skip-if-exists",
|
|
||||||
help="skip the download if file is already downloaded and file size is the same",
|
|
||||||
action="store_true",
|
|
||||||
)
|
|
||||||
download_parser.add_argument(
|
|
||||||
"-e", "--exclude", help="exclude to download path matched file or folders", action="append"
|
|
||||||
)
|
|
||||||
download_parser.add_argument("-p", "--password", help="password to use when open locked folder")
|
download_parser.add_argument("-p", "--password", help="password to use when open locked folder")
|
||||||
download_parser.add_argument("remote_path", help="remote file path (remote:/lab/path/file)")
|
download_parser.add_argument("remote_path", help="remote file path (remote:/lab/path/file)")
|
||||||
download_parser.add_argument("local_path", help="local folder path (/foo/bar/)")
|
download_parser.add_argument("local_path", help="local folder path (/foo/bar/)")
|
||||||
@ -52,21 +36,11 @@ class DownloadCommand(BaseCommand):
|
|||||||
remote_path = str(args.remote_path)
|
remote_path = str(args.remote_path)
|
||||||
local_path = str(args.local_path)
|
local_path = str(args.local_path)
|
||||||
is_recursive = bool(args.recursive)
|
is_recursive = bool(args.recursive)
|
||||||
is_skip_if_exists = bool(args.skip_if_exists)
|
|
||||||
password = str(args.password) if args.password else None
|
password = str(args.password) if args.password else None
|
||||||
excludes = list(map(lambda x: str(x).rstrip("/").lower(), args.exclude)) if args.exclude is not None else []
|
cls.download(remote_path, local_path, is_recursive, password)
|
||||||
cls.download(remote_path, local_path, is_recursive, is_skip_if_exists, password, excludes)
|
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def download(
|
def download(cls, remote_path: str, local_path: str, is_recursive: bool, password: str | None) -> None:
|
||||||
cls,
|
|
||||||
remote_path: str,
|
|
||||||
local_path: str,
|
|
||||||
is_recursive: bool,
|
|
||||||
is_skip_if_exists: bool,
|
|
||||||
password: str | None,
|
|
||||||
excludes: list[str],
|
|
||||||
) -> None:
|
|
||||||
(remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
|
(remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
|
||||||
r_path = r_path.rstrip("/")
|
r_path = r_path.rstrip("/")
|
||||||
r_dirname = os.path.dirname(r_path)
|
r_dirname = os.path.dirname(r_path)
|
||||||
@ -78,13 +52,10 @@ class DownloadCommand(BaseCommand):
|
|||||||
laboratory = cls._find_laboratory(connection, laboratory_name)
|
laboratory = cls._find_laboratory(connection, laboratory_name)
|
||||||
r_parent_folder = cls._find_folder(connection, laboratory, r_dirname, password)
|
r_parent_folder = cls._find_folder(connection, laboratory, r_dirname, password)
|
||||||
file = r_parent_folder.find_file(r_basename)
|
file = r_parent_folder.find_file(r_basename)
|
||||||
|
download_files: list[DownloadFileInfo] = []
|
||||||
if file is not None:
|
if file is not None:
|
||||||
if cls.__check_excludes(excludes, laboratory, r_parent_folder, file):
|
|
||||||
return
|
|
||||||
context = DownloadContext(False, is_skip_if_exists, [])
|
|
||||||
l_path = os.path.join(l_dirname, r_basename)
|
l_path = os.path.join(l_dirname, r_basename)
|
||||||
context.files.append(DownloadFileInfo(file, l_path))
|
download_files.append(DownloadFileInfo(file, l_path))
|
||||||
cls.__multiple_download(connection, context)
|
|
||||||
else:
|
else:
|
||||||
folder = r_parent_folder.find_sub_folder(r_basename)
|
folder = r_parent_folder.find_sub_folder(r_basename)
|
||||||
if folder is None:
|
if folder is None:
|
||||||
@ -92,67 +63,31 @@ class DownloadCommand(BaseCommand):
|
|||||||
if not is_recursive:
|
if not is_recursive:
|
||||||
raise IllegalArgumentException(f"Cannot download `{r_path}`: Is a folder.")
|
raise IllegalArgumentException(f"Cannot download `{r_path}`: Is a folder.")
|
||||||
folder_api = FoldersApi(connection)
|
folder_api = FoldersApi(connection)
|
||||||
cls.__multiple_download_pickup_recursive_files(
|
cls.__multiple_download_pickup_recursive_files(folder_api, download_files, folder.id, l_dirname)
|
||||||
connection, folder_api, laboratory, folder.id, l_dirname, excludes, is_skip_if_exists
|
cls.__multiple_download(connection, download_files)
|
||||||
)
|
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def __multiple_download_pickup_recursive_files(
|
def __multiple_download_pickup_recursive_files(
|
||||||
cls,
|
cls, folder_api: FoldersApi, infolist: list[DownloadFileInfo], folder_id: str, basedir: str
|
||||||
connection: MDRSConnection,
|
|
||||||
folder_api: FoldersApi,
|
|
||||||
laboratory: Laboratory,
|
|
||||||
folder_id: str,
|
|
||||||
basedir: str,
|
|
||||||
excludes: list[str],
|
|
||||||
is_skip_if_exists: bool,
|
|
||||||
) -> None:
|
) -> None:
|
||||||
context = DownloadContext(False, is_skip_if_exists, [])
|
|
||||||
folder = folder_api.retrieve(folder_id)
|
folder = folder_api.retrieve(folder_id)
|
||||||
dirname = os.path.join(basedir, folder.name)
|
dirname = os.path.join(basedir, folder.name)
|
||||||
if cls.__check_excludes(excludes, laboratory, folder, None):
|
|
||||||
return
|
|
||||||
if not os.path.exists(dirname):
|
if not os.path.exists(dirname):
|
||||||
os.makedirs(dirname)
|
os.makedirs(dirname)
|
||||||
print(dirname)
|
print(dirname)
|
||||||
for file in folder.files:
|
for file in folder.files:
|
||||||
if cls.__check_excludes(excludes, laboratory, folder, file):
|
|
||||||
continue
|
|
||||||
path = os.path.join(dirname, file.name)
|
path = os.path.join(dirname, file.name)
|
||||||
context.files.append(DownloadFileInfo(file, path))
|
infolist.append(DownloadFileInfo(file, path))
|
||||||
cls.__multiple_download(connection, context)
|
|
||||||
if context.hasError:
|
|
||||||
raise UnexpectedException("Some files failed to download.")
|
|
||||||
for sub_folder in folder.sub_folders:
|
for sub_folder in folder.sub_folders:
|
||||||
cls.__multiple_download_pickup_recursive_files(
|
cls.__multiple_download_pickup_recursive_files(folder_api, infolist, sub_folder.id, dirname)
|
||||||
connection, folder_api, laboratory, sub_folder.id, dirname, excludes, is_skip_if_exists
|
|
||||||
)
|
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def __multiple_download(cls, connection: MDRSConnection, context: DownloadContext) -> None:
|
def __multiple_download(cls, connection: MDRSConnection, infolist: list[DownloadFileInfo]) -> None:
|
||||||
file_api = FilesApi(connection)
|
file_api = FilesApi(connection)
|
||||||
with ThreadPoolExecutor(max_workers=CONCURRENT) as pool:
|
with ThreadPoolExecutor(max_workers=CONCURRENT) as pool:
|
||||||
results = pool.map(
|
pool.map(lambda x: cls.__multiple_download_worker(file_api, x), infolist)
|
||||||
lambda x: cls.__multiple_download_worker(file_api, x, context.isSkipIfExists), context.files
|
|
||||||
)
|
|
||||||
hasError = next(filter(lambda x: x is False, results), None)
|
|
||||||
if hasError is not None:
|
|
||||||
context.hasError = True
|
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def __multiple_download_worker(cls, file_api: FilesApi, info: DownloadFileInfo, is_skip_if_exists: bool) -> bool:
|
def __multiple_download_worker(cls, file_api: FilesApi, info: DownloadFileInfo) -> None:
|
||||||
if not is_skip_if_exists or os.path.exists(info.path) and info.file.size != os.path.getsize(info.path):
|
file_api.download(info.file, info.path)
|
||||||
try:
|
|
||||||
file_api.download(info.file, info.path)
|
|
||||||
except Exception:
|
|
||||||
print(f"Failed: ${info.path}")
|
|
||||||
if os.path.isfile(info.path):
|
|
||||||
os.remove(info.path)
|
|
||||||
return False
|
|
||||||
print(info.path)
|
print(info.path)
|
||||||
return True
|
|
||||||
|
|
||||||
@classmethod
|
|
||||||
def __check_excludes(cls, excludes: list[str], laboratory: Laboratory, folder: Folder, file: File | None) -> bool:
|
|
||||||
path = f"/{laboratory.name}{folder.path}{file.name if file is not None else ''}".rstrip("/").lower()
|
|
||||||
return path in excludes
|
|
||||||
|
@ -26,12 +26,6 @@ class UploadCommand(BaseCommand):
|
|||||||
upload_parser.add_argument(
|
upload_parser.add_argument(
|
||||||
"-r", "--recursive", help="upload directories and their contents recursive", action="store_true"
|
"-r", "--recursive", help="upload directories and their contents recursive", action="store_true"
|
||||||
)
|
)
|
||||||
upload_parser.add_argument(
|
|
||||||
"-s",
|
|
||||||
"--skip-if-exists",
|
|
||||||
help="skip the upload if file is already uploaded and file size is the same",
|
|
||||||
action="store_true",
|
|
||||||
)
|
|
||||||
upload_parser.add_argument("local_path", help="local file path (/foo/bar/data.txt)")
|
upload_parser.add_argument("local_path", help="local file path (/foo/bar/data.txt)")
|
||||||
upload_parser.add_argument("remote_path", help="remote folder path (remote:/lab/path/)")
|
upload_parser.add_argument("remote_path", help="remote folder path (remote:/lab/path/)")
|
||||||
upload_parser.set_defaults(func=cls.func)
|
upload_parser.set_defaults(func=cls.func)
|
||||||
@ -41,11 +35,10 @@ class UploadCommand(BaseCommand):
|
|||||||
local_path = str(args.local_path)
|
local_path = str(args.local_path)
|
||||||
remote_path = str(args.remote_path)
|
remote_path = str(args.remote_path)
|
||||||
is_recursive = bool(args.recursive)
|
is_recursive = bool(args.recursive)
|
||||||
is_skip_if_exists = bool(args.skip_if_exists)
|
cls.upload(local_path, remote_path, is_recursive)
|
||||||
cls.upload(local_path, remote_path, is_recursive, is_skip_if_exists)
|
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def upload(cls, local_path: str, remote_path: str, is_recursive: bool, is_skip_if_exists: bool) -> None:
|
def upload(cls, local_path: str, remote_path: str, is_recursive: bool) -> None:
|
||||||
(remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
|
(remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
|
||||||
l_path = os.path.abspath(local_path)
|
l_path = os.path.abspath(local_path)
|
||||||
if not os.path.exists(l_path):
|
if not os.path.exists(l_path):
|
||||||
@ -85,25 +78,23 @@ class UploadCommand(BaseCommand):
|
|||||||
infos.append(UploadFileInfo(folder_map[d_dirname], os.path.join(dirpath, filename)))
|
infos.append(UploadFileInfo(folder_map[d_dirname], os.path.join(dirpath, filename)))
|
||||||
else:
|
else:
|
||||||
infos.append(UploadFileInfo(folder, l_path))
|
infos.append(UploadFileInfo(folder, l_path))
|
||||||
cls.__multiple_upload(connection, infos, is_skip_if_exists)
|
cls.__multiple_upload(connection, infos)
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def __multiple_upload(
|
def __multiple_upload(cls, connection: MDRSConnection, infos: list[UploadFileInfo]) -> None:
|
||||||
cls, connection: MDRSConnection, infos: list[UploadFileInfo], is_skip_if_exists: bool
|
|
||||||
) -> None:
|
|
||||||
file_api = FilesApi(connection)
|
file_api = FilesApi(connection)
|
||||||
with ThreadPoolExecutor(max_workers=CONCURRENT) as pool:
|
with ThreadPoolExecutor(max_workers=CONCURRENT) as pool:
|
||||||
pool.map(lambda x: cls.__multiple_upload_worker(file_api, x, is_skip_if_exists), infos)
|
pool.map(lambda x: cls.__multiple_upload_worker(file_api, x), infos)
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def __multiple_upload_worker(cls, file_api: FilesApi, info: UploadFileInfo, is_skip_if_exists: bool) -> None:
|
def __multiple_upload_worker(cls, file_api: FilesApi, info: UploadFileInfo) -> None:
|
||||||
basename = os.path.basename(info.path)
|
basename = os.path.basename(info.path)
|
||||||
file = info.folder.find_file(basename)
|
file = info.folder.find_file(basename)
|
||||||
try:
|
try:
|
||||||
if file is None:
|
if file is None:
|
||||||
file_api.create(info.folder.id, info.path)
|
file_api.create(info.folder.id, info.path)
|
||||||
elif not is_skip_if_exists or file.size != os.path.getsize(info.path):
|
else:
|
||||||
file_api.update(file, info.path)
|
file_api.update(file, info.path)
|
||||||
print(os.path.join(info.folder.path, basename))
|
print(os.path.join(info.folder.path, basename))
|
||||||
except MDRSException as e:
|
except MDRSException as e:
|
||||||
print(f"Error: {e}")
|
print(f"API Error: {e}")
|
||||||
|
@ -2,7 +2,7 @@ import configparser
|
|||||||
import os
|
import os
|
||||||
from typing import Final
|
from typing import Final
|
||||||
|
|
||||||
import validators
|
import validators # type: ignore
|
||||||
|
|
||||||
from mdrsclient.exceptions import IllegalArgumentException
|
from mdrsclient.exceptions import IllegalArgumentException
|
||||||
from mdrsclient.settings import CONFIG_DIRNAME
|
from mdrsclient.settings import CONFIG_DIRNAME
|
||||||
@ -41,7 +41,7 @@ class ConfigFile:
|
|||||||
|
|
||||||
@url.setter
|
@url.setter
|
||||||
def url(self, url: str) -> None:
|
def url(self, url: str) -> None:
|
||||||
if not validators.url(url):
|
if not validators.url(url): # type: ignore
|
||||||
raise IllegalArgumentException("malformed URI sequence")
|
raise IllegalArgumentException("malformed URI sequence")
|
||||||
self.__load()
|
self.__load()
|
||||||
if self.__config.has_section(self.remote):
|
if self.__config.has_section(self.remote):
|
||||||
|
@ -1,9 +1,9 @@
|
|||||||
import platform
|
import platform
|
||||||
import threading
|
import threading
|
||||||
|
from io import BufferedReader
|
||||||
from typing import TypedDict
|
from typing import TypedDict
|
||||||
|
|
||||||
from requests import Response, Session
|
from requests import Response, Session
|
||||||
from requests_toolbelt.multipart.encoder import MultipartEncoder
|
|
||||||
|
|
||||||
# Unpack is new in 3.11
|
# Unpack is new in 3.11
|
||||||
from typing_extensions import Unpack
|
from typing_extensions import Unpack
|
||||||
@ -21,14 +21,14 @@ class _KwArgsMDRSConnectionGet(TypedDict, total=False):
|
|||||||
|
|
||||||
class _KwArgsMDRSConnectionPost(TypedDict, total=False):
|
class _KwArgsMDRSConnectionPost(TypedDict, total=False):
|
||||||
params: dict[str, str | int]
|
params: dict[str, str | int]
|
||||||
data: dict[str, str | int] | MultipartEncoder
|
data: dict[str, str | int]
|
||||||
headers: dict[str, str]
|
files: dict[str, BufferedReader]
|
||||||
|
|
||||||
|
|
||||||
class _KwArgsMDRSConnectionPut(TypedDict, total=False):
|
class _KwArgsMDRSConnectionPut(TypedDict, total=False):
|
||||||
params: dict[str, str | int]
|
params: dict[str, str | int]
|
||||||
data: dict[str, str | int] | MultipartEncoder
|
data: dict[str, str | int]
|
||||||
headers: dict[str, str]
|
files: dict[str, BufferedReader]
|
||||||
|
|
||||||
|
|
||||||
class _KwArgsMDRSConnectionDelete(TypedDict, total=False):
|
class _KwArgsMDRSConnectionDelete(TypedDict, total=False):
|
||||||
|
@ -1,6 +1,6 @@
|
|||||||
[tool.poetry]
|
[tool.poetry]
|
||||||
name = "mdrs-client-python"
|
name = "mdrs-client-python"
|
||||||
version = "1.3.11"
|
version = "1.3.2"
|
||||||
description = "The mdrs-client-python is python library and a command-line client for up- and downloading files to and from MDRS based repository."
|
description = "The mdrs-client-python is python library and a command-line client for up- and downloading files to and from MDRS based repository."
|
||||||
authors = ["Yoshihiro OKUMURA <yoshihiro.okumura@riken.jp>"]
|
authors = ["Yoshihiro OKUMURA <yoshihiro.okumura@riken.jp>"]
|
||||||
license = "MIT"
|
license = "MIT"
|
||||||
@ -13,7 +13,6 @@ classifiers=[
|
|||||||
"Programming Language :: Python :: 3.10",
|
"Programming Language :: Python :: 3.10",
|
||||||
"Programming Language :: Python :: 3.11",
|
"Programming Language :: Python :: 3.11",
|
||||||
"Programming Language :: Python :: 3.12",
|
"Programming Language :: Python :: 3.12",
|
||||||
"Programming Language :: Python :: 3.13",
|
|
||||||
"OSI Approved :: MIT License",
|
"OSI Approved :: MIT License",
|
||||||
"Topic :: Utilities",
|
"Topic :: Utilities",
|
||||||
]
|
]
|
||||||
@ -23,20 +22,19 @@ packages = [
|
|||||||
|
|
||||||
[tool.poetry.dependencies]
|
[tool.poetry.dependencies]
|
||||||
python = "^3.10"
|
python = "^3.10"
|
||||||
requests = "^2.32.3"
|
requests = "^2.31.0"
|
||||||
requests-toolbelt = "^1.0.0"
|
python-dotenv = "^1.0.0"
|
||||||
python-dotenv = "^1.0.1"
|
pydantic = "^2.5.2"
|
||||||
pydantic = "^2.10.5"
|
pydantic-settings = "^2.1.0"
|
||||||
pydantic-settings = "^2.7.1"
|
PyJWT = "^2.8.0"
|
||||||
PyJWT = "^2.10.1"
|
validators = "^0.22.0"
|
||||||
validators = "^0.34.0"
|
|
||||||
|
|
||||||
[tool.poetry.group.dev.dependencies]
|
[tool.poetry.group.dev.dependencies]
|
||||||
black = "^24.10.0"
|
black = "^24.1.1"
|
||||||
flake8 = "^7.1.1"
|
flake8 = "^7.0.0"
|
||||||
Flake8-pyproject = "^1.2.3"
|
Flake8-pyproject = "^1.2.3"
|
||||||
isort = "^5.13.2"
|
isort = "^5.13.0"
|
||||||
pyright = "^1.1.391"
|
pyright = "^1.1.339"
|
||||||
|
|
||||||
[tool.poetry.scripts]
|
[tool.poetry.scripts]
|
||||||
mdrs = 'mdrsclient.__main__:main'
|
mdrs = 'mdrsclient.__main__:main'
|
||||||
|
Loading…
x
Reference in New Issue
Block a user